GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagEcb in Pseudomonas fluorescens GW456-L13

Align N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized)
to candidate PfGW456L13_4833 PTS system, N-acetylglucosamine-specific IIA component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIB component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIC component (EC 2.7.1.69)

Query= reanno::pseudo3_N2E3:AO353_04465
         (571 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4833
          Length = 571

 Score =  993 bits (2566), Expect = 0.0
 Identities = 495/571 (86%), Positives = 534/571 (93%)

Query: 1   MYQLFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAIIHDAGQVIFANLALIFAI 60
           MYQLFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAIIHDAGQVIFANLA+IFAI
Sbjct: 1   MYQLFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAIIHDAGQVIFANLAMIFAI 60

Query: 61  GIAVGFARDNNGTAGLAGAIGYLVMVSTLKVLDASINMGMLAGIISGLMAGALYNRFKDI 120
           GIAVGFARDNNGTAGLAG IGYLVM+STLK LD SINMGMLAGI+SGLMAGALYNRFKDI
Sbjct: 61  GIAVGFARDNNGTAGLAGVIGYLVMISTLKALDPSINMGMLAGIVSGLMAGALYNRFKDI 120

Query: 121 KLPEYLAFFGGRRFVPIATGFSAVGLGVIFGLIWPPIQHGINSFGQLLLESGSIGAFVFG 180
           KLPEYLAFFGGRRFVPI TGF+AVGLGV+FG IWPPIQHGINSFG L++ESGS GAFVFG
Sbjct: 121 KLPEYLAFFGGRRFVPIVTGFAAVGLGVVFGYIWPPIQHGINSFGTLMMESGSFGAFVFG 180

Query: 181 VFNRLLIVTGLHHILNNMAWFIFGSFTDPTTGAIVTGDLARYFAGDPKGGQFMTGMFPMM 240
           +FNRLLIVTGLHHILNNMAWF+FG+FTDPTTGA+VTGDL+RYFAGDPKGGQFMTGMFPMM
Sbjct: 181 LFNRLLIVTGLHHILNNMAWFVFGNFTDPTTGALVTGDLSRYFAGDPKGGQFMTGMFPMM 240

Query: 241 IFGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPLLYLLHVL 300
           IFGLPAACLAMYRNALP RRKVMGGIFLSMALT+FLTGVTEPIEFAFMFLAPLL++LH L
Sbjct: 241 IFGLPAACLAMYRNALPARRKVMGGIFLSMALTAFLTGVTEPIEFAFMFLAPLLFVLHAL 300

Query: 301 LTGMAMAITNALNIHLGFTFSGGAIDMALGWGKSTNGWLVFPVGLAYAVIYYVVFDFCIR 360
           LTG++MAITNALNIHLGFTFSGG IDM LGWGKSTNGWLVFPVGLAYAVIYYVVFDFCIR
Sbjct: 301 LTGLSMAITNALNIHLGFTFSGGFIDMILGWGKSTNGWLVFPVGLAYAVIYYVVFDFCIR 360

Query: 361 RFNLKTPGREGVVVGEKVVLSENQRAGAYIQALGGAENLITVGACTTRLRLEMVDRNKAS 420
           RF+LKTPGRE     E+V +++N+RAGAYI+ALGGAENLITVGACTTRLRL+MVDRNKAS
Sbjct: 361 RFDLKTPGRETSADVEQVAVADNERAGAYIKALGGAENLITVGACTTRLRLDMVDRNKAS 420

Query: 421 DSELKALGAMAVVRPGKGGSLQVVVGPLADSIADEIRQAMPTAGSALVAAVVVTEEAPKA 480
           D++LKALGAMAVVRPGKGGSLQVVVGP+AD+IADEIR AMP  G A+V++     +AP  
Sbjct: 421 DTDLKALGAMAVVRPGKGGSLQVVVGPMADAIADEIRLAMPALGRAMVSSPAAEIDAPPP 480

Query: 481 APVETPEAQKWLNAVGGSDNVLQLDCVAMTRIRLQLADGKALSECQLKDLGCQGVSALDG 540
           A + TPEAQ+WLNA+GG DNVLQLDCVAMTRIRLQLADGKALSE  LK LGCQGVS LDG
Sbjct: 481 AAMATPEAQQWLNALGGGDNVLQLDCVAMTRIRLQLADGKALSEFDLKALGCQGVSQLDG 540

Query: 541 GVWHLLIGDKALSLSEALEGLVNRSEVSAKV 571
           G+WHLLIGDKA +LS+ALE LVNRSEVSAKV
Sbjct: 541 GIWHLLIGDKAPTLSDALEVLVNRSEVSAKV 571


Lambda     K      H
   0.325    0.142    0.421 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1190
Number of extensions: 53
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 571
Length of database: 571
Length adjustment: 36
Effective length of query: 535
Effective length of database: 535
Effective search space:   286225
Effective search space used:   286225
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory